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Here is the recon-all.log file.
Thanks, Elana
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Today's Topics:
1. FS 7.1.0 - Editing intensity values for WM (Nils B?er) 2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce) 3. Creating .annot file for a mri_decimate downsampeld version of pial surface (Donelson Berger) 4. GONE: -make to recon-all (Johnson, Hans J) 5. Re: fsgd file - glmfit error (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience) 6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.) 7. bad interpreter: No such file or directory error (Hengameh Marzbani) 8. Re: overlapping/ superimposing regions of one analysis over another (Douglas N. Greve) 9. Re: Creating .annot file for a mri_decimate downsampeld version of pial surface (Douglas N. Greve) 10. Re: Recon-all Soft Errors (Douglas N. Greve) 11. Re: Coregistration to MNI (Douglas N. Greve) 12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji) 13. Re: bad interpreter: No such file or directory error (fsbuild)
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Message: 1 Date: Wed, 29 Jul 2020 21:27:03 +0200 From: Nils B?er nils.tobias94@gmail.com Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: freesurfer@nmr.mgh.harvard.edu Message-ID: CALZW1G2=-OvWkL81sZxTBiMCKBwiOn6EwSfd2xP0NzEWQYBSTw@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hello everyone,
I just have a short question, because I can't find anything helpful in the tutorials.
In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that.
I'd be thankful for any feedback/links to guides.
Best regards,
Nils --
Nils B?er Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401
Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.de nils.tobias94@gmail.com Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
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Message: 2 Date: Wed, 29 Jul 2020 20:32:34 +0000 From: "Fischl, Bruce" BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BL0PR04MB660985EC505DEECB596362ADEF700@BL0PR04MB6609.namprd04.prod.outlook.com
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Hi Nils
There are expert options for this. You can specify things like -min_white 90 to some of the programs like mri_segment and the surface placement stuff
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Nils B?er Sent: Wednesday, July 29, 2020 3:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM
External Email - Use Caution Hello everyone,
I just have a short question, because I can't find anything helpful in the tutorials.
In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that.
I'd be thankful for any feedback/links to guides.
Best regards,
Nils --
Nils B?er Research Assistant with Bachelor Degree (WHB) Psychology and Movement University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.demailto:nils.tobias94@gmail.com Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animat...]https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail Virenfrei. www.avast.comhttps://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
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Message: 3 Date: Wed, 29 Jul 2020 15:51:03 -0500 From: Donelson Berger donelsongrahamberger@gmail.com Subject: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAAKWbtXL5vQOPXEoO6TUeRM_dHowghOYVX=ptXWPE8+GkAMENA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hello FreeSurfer Expert,
I've run into a problem that I just can't seem to solve. After downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces and 10,002 points, I don't know how to create .annot files for the new surfaces I created. I want to be able to tell which ROI each vertex is in for my new surface based off a parcellation.
I've been trying to use mri_ca_label, mri_ca_train, and mris_sample_parc, but I can't seem to get anything to work.
Do you have any suggestions?
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Message: 4 Date: Wed, 29 Jul 2020 22:22:47 +0000 From: "Johnson, Hans J" hans-johnson@uiowa.edu Subject: [Freesurfer] GONE: -make to recon-all To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 9DB20083-D647-47E0-9396-C24308B503B9@uiowa.edu Content-Type: text/plain; charset="utf-8"
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The release notes for 7.0.0 claim that the -make option is "Gone" from recon-all. This option, however, is still available and does not seem to fail.
I am running several thousand data sets on a cluster through Freesurfer 7.1.0, and periodically the process fails for some subjects. In the past the "recon-all -make all" feature was a very convenient way to complete freesurfer runs that were terminated early for some unknown reason
Q1) should "recon-all -make all" be avoided for FreeSurfer 7.1.0? Q2) is there an alternate way to "continue form the point where results are missing" in the pipeline?
Thanks, Hans
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Message: 5 Date: Wed, 29 Jul 2020 15:49:44 -0700 From: "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" ladn@email.gwu.edu Subject: Re: [Freesurfer] fsgd file - glmfit error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CACE7MB+VaV5UyPsnRSfnyDA8XT0_dDhe1sxd2-rumCf3z0_PDA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Thank you Douglas!
On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Try putting 1 after GroupDescriptorFile, ie,
GroupDescriptorFile 1
On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionHere is my fsgd file. Thank you!
On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Please send the fsgd file
On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
Hope this email finds you well. I am having some trouble with the fsgd file for glmfit and I'm confused why. This is the error I'm getting when running glmfit:
iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_BNB.00.mgh --fsgd fsgd_8.fsgd --C Cor_2.mtx --surf fsaverage rh --cortex --glmdir contrast2.rh_volume_BNB.glmdir gdfRead(): reading fsgd_8.fsgd ERROR: FSGDF version 0 unsupported (fsgd_8.fsgd) iMac-Pro:BAP_complete ajobsaid$
If needed, I can send you my fsgd file, but I have triple checked the design and format of the file (it is saved as .fsgd), and I'm still getting this error message.
Thank you, Alex
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Message: 6 Date: Thu, 30 Jul 2020 09:34:12 +0000 From: "Zollei, Lilla,Ph.D." LZOLLEI@mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Soft Errors To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: DM6PR04MB44127C2DB157BB07AB669F41E3710@DM6PR04MB4412.namprd04.prod.outlook.com
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Hi Elena, What is the age range of your subjects? Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Elana Sarabin elana.sarabin1@ucalgary.ca Sent: Wednesday, July 29, 2020 11:02 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all Soft Errors
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Hi Freesurfer experts,
I am a first time user of FreeSurfer and I haven?t been able to find any threads for how to fix some of my problems. I have a very large dataset and as I am editing on freeview I am noticing that ? or more of my participants have a large area missing in the brainmask.mgz file but the region is visible from the T1.file. In some participant scans the areas missing arent too big however other scans (the photo I attached) have a very large portion of the brain missing. I have tried quite a few things to fix this including re running recon-all, adding control points, and adjusting the wsthresh value, however, none have worked. Wondering if there is a way to fix this kind of error and if there is a way to prevent this from happening as I run recon-all on future participants. In addition, I have been duplicating my files before editing in order to always have the original files as a backup. With some participants when I duplicate the files their T1.mgz file ends up completely white (image attached). I have yet to see this in a none duplicated file however with some participants I can duplicate the files and have no issue. I have attached photos of both of my problems. Any suggestions for fixes would be greatly appreciated.
Thanks,
Elana
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Message: 7 Date: Thu, 30 Jul 2020 17:49:49 +0430 From: Hengameh Marzbani marzbani91@gmail.com Subject: [Freesurfer] bad interpreter: No such file or directory error To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CAFn2Bowe=LPArymmLwu=K_3WgEZC0GnG9OkV5qAeBPdZuGV8zw@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hello Freesurfer developers,
I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine.
Also, freeview works by simply typing the freeview command.
However,I have tried to run recon-all. but, I have got the following error message on all PCs:
*bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory*
also The build-stamps.txt file contents: *freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b*
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Message: 8 Date: Thu, 30 Jul 2020 10:20:07 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another To: freesurfer@nmr.mgh.harvard.edu Message-ID: c4e336e0-b3b8-89eb-e59b-1894fdf856b8@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
To obtain the common regions, first binarize the clusterwise significance maps with something like mri_binarize --min 2.0 --i clustersigmap1.mgh --o bin.clustersigmap1.mgh Same for the other groups Then take the intersection fscalc clustersigmap1.mgh and clustersigmap2.mgh -o intersection.mgh
On 7/27/2020 2:17 PM, Sunil Khokhar wrote:
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To operate the visualization and obtain the common regions of my between-group difference results and the correlation results in one image. In other?words, overlapping/ superimposing?my correlation results on the between-group results (to obtain the common regions from the two separate analysis).
Thanks _______________ Sunil K Khokhar PhD Scholar, Department of Neuroimaging & Interventional Radiology, NIMHANS, Bengaluru, INDIA. khokharsunil1@gmail.com mailto:khokharsunil1@gmail.com +91-9413101839
On Mon, Jul 27, 2020 at 8:21 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
are you asking how to create positive and negative regions or are you asking how to operate the visualization? On 7/25/2020 9:40 AM, Sunil Khokhar wrote:????????External Email - Use Caution Dear Experts, I have done a between group (2 groups) difference in whole brain voxel based cortical thickness using QDEC, which showed significant regional differences in certain clusters bilaterally?in the brain. I also did a correlation between cortical thickness and behavioral scores separately?in these two groups. Now, I want to superimpose regions (clusters) which showed positive and negative correlation on the?results/ regions?I obtained in my between group analysis. How can I do this? Thanks in advance! Sunil. _______________ Sunil K Khokhar PhD Scholar, Department of Neuroimaging & Interventional Radiology, NIMHANS, Bengaluru, INDIA. khokharsunil1@gmail.com <mailto:khokharsunil1@gmail.com> +91-9413101839 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 9 Date: Thu, 30 Jul 2020 10:21:14 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Creating .annot file for a mri_decimate downsampeld version of pial surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: ec2eef74-6cd8-0c36-dbeb-983240090223@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Use mris_apply_reg --sval-annot lh.your.annot --streg lh.pial lh.pial.decimated --o lh.your.decimated.annot
On 7/29/2020 4:51 PM, Donelson Berger wrote:
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Hello FreeSurfer Expert,
I've run into a problem that I just can't seem to solve. After downsampling teh ?.pial surfaces using mri_decimate to 20,000 surfaces and 10,002 points, I don't know how to create .annot files for the new surfaces I created. I want to be able to tell which ROI each vertex is in for my new surface based off a parcellation.
I've been trying to use mri_ca_label, mri_ca_train, and mris_sample_parc, but I can't seem to get anything to work.
Do you have any suggestions?
Thanks for your help, Donelson Graham Berger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 10 Date: Thu, 30 Jul 2020 10:26:22 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Soft Errors To: freesurfer@nmr.mgh.harvard.edu Message-ID: 78c6cfdd-63ba-9ed1-1c26-fcbc76472ac8@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
for the first error, can you send the recon-all.log file? For the second error, you need to adjust the intensity ranges. For some reason they are coming up as 0s.
On 7/29/2020 11:02 AM, Elana Sarabin wrote:
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Hi Freesurfer experts,
I am a first time user of FreeSurfer and I haven?t been able to find any threads for how to fix some of my problems. I have a very large dataset and as I am editing on freeview I am noticing that ? or more of my participants have a large area missing in the brainmask.mgz file but the region is visible from the T1.file. In some participant scans the areas missing arent too big however other scans (the photo I attached) have a very large portion of the brain missing. I have tried quite a few things to fix this including re running recon-all, adding control points, and adjusting the wsthresh value, however, none have worked. Wondering if there is a way to fix this kind of error and if there is a way to prevent this from happening as I run recon-all on future participants. In addition, I have been duplicating my files before editing in order to always have the original files as a backup. With some participants when I duplicate the files their T1.mgz file ends up completely white (image attached). I have yet to see this in a none duplicated file however with some participants I can duplicate the files and have no issue. I have attached photos of both of my problems. Any suggestions for fixes would be greatly appreciated.
Thanks,
Elana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 11 Date: Thu, 30 Jul 2020 11:31:47 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Coregistration to MNI To: "Camargo, Aldo" ACamargo@som.umaryland.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 9af8c73e-46a8-e9b6-4b84-ce507589efed@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
It looks like cvs failed. Can you send the log? Also, please remember to post to the list and not us personally.
On 7/30/2020 11:13 AM, Camargo, Aldo wrote:
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Hi Douglas,
I was able to run the script to create the cvs folder and its files but still I can not run the script that does the coregistration of the Pet image to the MNI space.
I am getting the following error:
(base) acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46 .0/S19445/subj1/mri$ mri_vol2vol --gcam /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me anPET.nii.gz register.dof6.lta $SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.ni.gz Loading mov /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/me anPET.nii.gz Loading source LTA register.dof6.lta Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z ERROR: cannot find or read /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
-- *From:* Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, July 29, 2020 10:39 AM *To:* Camargo, Aldo ACamargo@som.umaryland.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Coregistration to MNI Here is the command mri_cvs_register --mov $subject --mni --openmp N
This command can take a very long time to run. The --openmp N indicates the number of processors to use if you have a multiprocessor system. Even with N=3, it can take 18 hours.
On 7/29/2020 12:35 AM, Camargo, Aldo wrote:
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Hi Douglas,
I don't have the folder cvs and I don't have the files bellow:
cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
How can I get these files,
Aldo
*From:* Camargo, Aldo ACamargo@som.umaryland.edu mailto:ACamargo@som.umaryland.edu *Sent:* Monday, July 27, 2020 11:46 PM *To:* Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot Douglas for your great input,
Aldo
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, July 27, 2020 10:46 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Coregistration to MNI This command will allow you to have a registration file and sample into MNI152 2mm space
mri_vol2vol --gcam pet.nii.gz register.dof6.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.nii.gz
you can get the registration file with mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta
On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote:
Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camargo, Aldo ACamargo@som.umaryland.edu mailto:ACamargo@som.umaryland.edu *Sent:* Saturday, July 25, 2020 12:19 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Coregistration to MNI
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Hi Freesurfer experts,
I want to coregister a PET image to the MNI space, can I use mri_cvs_register ?
Thanks a lot,
Aldo Camargo
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Message: 12 Date: Thu, 30 Jul 2020 17:39:06 +0200 From: Ellen Ji ellen.ji@bli.uzh.ch Subject: [Freesurfer] mri_aparc2aseg: how to remove redundant output labels? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 24cc8874-81ee-1e68-85ad-b8fe662c4fc3@bli.uzh.ch Content-Type: text/plain; charset="utf-8"; format="flowed"
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Dear experts,
I am running mri_aparc2aseg using two annotations as input (one for each hemisphere), each with 159 labels, and wish to end up with a single output segmentation of 318 labels. However, when I run the below, this is not the case:
mri_aparc2aseg \ ??????????????? --s subject1 \ ??????????????? --annot 500_sym.aparc \ ??????????????? --wmparc-dmax 2 \ ??????????????? --labelwm \ ??????????????? --hypo-as-wm? \ ??????????????? --o subject1/mri/parcellation.nii.gz
In fact, the output has 680 labels rather than 318 labels. A few questions.
- How can I see what exactly the 680 label names are (how to extract from the .nii.gz output file)? Currently, I have just quantified it to be 680 by doing this in matlab: gunzip('parcellation.nii.gz') ???? a = MRIread('parcellation.nii'); ???? u = unique(a.vol(:)); ???? length(u) % total number of labels
- I believe the extra labels are from the Freesurfer LUT. How can I make sure they are not added when running mri_aparc2aseg? (such that only my annotation labels are included in the output)
Thank you very much,
Ellen
***** Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Z?rich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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Message: 13 Date: Thu, 30 Jul 2020 17:48:25 +0200 From: fsbuild fsbuild@contbay.com Subject: Re: [Freesurfer] bad interpreter: No such file or directory error To: freesurfer@nmr.mgh.harvard.edu Cc: marzbani91@gmail.com Message-ID: 1596124105.5f22ebc98f04a@trashmail.com Content-Type: text/plain; charset="utf-8"
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Hello Hengameh, You probably need to install tcsh (and or csh). I would try, $ sudo apt-get install csh tcsh - R..
On Jul 30, 2020, at 09:19, Hengameh Marzbani <marzbani91@gmail.com> wrote: External Email - Use Caution Hello Freesurfer developers,I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command.However,I have tried to run recon-all. but, I have got the following error message on all PCs:bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directoryalso The build-stamps.txt file contents:freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297bThank you in advance, Best regards, Hengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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End of Freesurfer Digest, Vol 197, Issue 59 *******************************************